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{{f5samples
{{f5samples
|F5samples=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000084,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000827,CL:0000837,CL:0000838,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000084,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000827,CL:0000837,CL:0000838,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=FF:0100104
|fonse_cell_line=FF:0100104
|fonse_cell_line_closure=FF:0100104
|fonse_cell_line_closure=FF:0100104

Revision as of 16:57, 29 March 2012


Name:mycosis fungoides, T cell lymphoma cell line:HuT 102 TIB-162
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
age26
cell typet cell
cell lineHuT 102 TIB-162
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis0.0794
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma0.388
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
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C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11858

Jaspar motifP-value
MA0002.20.00575
MA0003.10.879
MA0004.10.35
MA0006.10.736
MA0007.10.434
MA0009.10.816
MA0014.10.466
MA0017.10.107
MA0018.20.306
MA0019.10.828
MA0024.12.62457e-5
MA0025.10.0664
MA0027.10.771
MA0028.10.0105
MA0029.10.906
MA0030.10.197
MA0031.10.659
MA0035.20.0111
MA0038.10.741
MA0039.20.448
MA0040.10.116
MA0041.10.213
MA0042.10.408
MA0043.10.244
MA0046.10.228
MA0047.20.405
MA0048.10.436
MA0050.12.80035e-12
MA0051.12.78462e-9
MA0052.10.482
MA0055.10.442
MA0057.10.98
MA0058.10.563
MA0059.10.167
MA0060.15.81505e-6
MA0061.11.45956e-14
MA0062.21.07386e-6
MA0065.20.0102
MA0066.10.861
MA0067.10.528
MA0068.10.674
MA0069.10.793
MA0070.10.66
MA0071.10.68
MA0072.10.296
MA0073.10.534
MA0074.10.815
MA0076.10.00424
MA0077.10.354
MA0078.10.758
MA0079.20.957
MA0080.24.85116e-6
MA0081.10.31
MA0083.10.0237
MA0084.10.19
MA0087.10.0582
MA0088.10.0942
MA0090.14.92665e-8
MA0091.10.518
MA0092.10.872
MA0093.10.429
MA0099.20.816
MA0100.10.0327
MA0101.16.21034e-13
MA0102.20.344
MA0103.10.954
MA0104.20.0725
MA0105.11.48622e-12
MA0106.10.00486
MA0107.14.42738e-13
MA0108.20.0609
MA0111.10.262
MA0112.20.911
MA0113.10.623
MA0114.10.0206
MA0115.10.747
MA0116.18.89092e-5
MA0117.10.219
MA0119.10.909
MA0122.10.831
MA0124.10.528
MA0125.10.98
MA0131.10.0824
MA0135.10.0921
MA0136.18.34417e-7
MA0137.20.253
MA0138.20.453
MA0139.10.337
MA0140.10.135
MA0141.10.0451
MA0142.10.306
MA0143.10.168
MA0144.10.415
MA0145.10.852
MA0146.10.188
MA0147.10.0441
MA0148.10.665
MA0149.10.199
MA0150.10.75
MA0152.10.0768
MA0153.10.00608
MA0154.10.00505
MA0155.10.591
MA0156.18.68211e-7
MA0157.10.521
MA0159.10.284
MA0160.10.0604
MA0162.10.467
MA0163.11.16377e-6
MA0164.10.887
MA0258.10.185
MA0259.10.59



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs11858

Novel motifP-value
10.0208
100.0219
1000.325
1010.114
1020.358
1030.0796
1040.77
1050.21
1060.379
1070.423
1080.679
1090.0165
110.113
1100.409
1110.0866
1120.13
1130.526
1140.267
1150.359
1160.131
1170.0259
1180.904
1190.126
120.396
1200.539
1210.389
1220.218
1232.20598e-4
1240.218
1250.299
1260.809
1270.115
1280.779
1290.285
130.254
1300.548
1310.98
1320.501
1330.564
1340.578
1350.0387
1360.199
1370.904
1380.704
1390.854
140.444
1400.558
1410.786
1420.813
1430.00195
1440.282
1450.803
1460.308
1470.0494
1480.00492
1490.379
150.136
1500.428
1510.93
1520.938
1530.599
1540.556
1550.187
1560.207
1570.445
1580.732
1590.124
160.686
1600.323
1610.225
1620.129
1630.417
1640.52
1650.781
1660.642
1670.407
1680.827
1690.997
170.534
180.494
190.837
20.678
200.424
210.208
220.815
230.381
240.295
250.0563
260.124
270.371
280.332
290.0152
30.203
300.0387
310.773
320.511
330.915
340.488
350.513
360.0228
370.112
380.91
390.316
40.106
400.223
410.794
420.0894
430.453
440.033
450.225
460.309
470.12
480.356
490.252
50.794
500.569
510.534
520.503
530.324
540.819
550.0494
560.899
570.27
580.0639
590.672
60.827
600.616
610.444
620.0831
630.975
640.159
650.718
660.0148
670.158
680.134
690.273
70.285
700.465
710.0309
720.3
730.357
740.395
750.114
760.748
770.348
780.0147
790.451
80.406
800.396
810.273
820.53
830.0818
840.1
850.99
860.135
870.0246
880.488
890.494
90.926
900.666
910.838
920.581
930.154
940.457
950.00261
960.023
970.132
980.997
990.0934



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs11858


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000084 (T cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0060058 (lymphoma)
0060060 (non-Hodgkin lymphoma)
0060061 (cutaneous T cell lymphoma)
0060083 (immune system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2531 (hematologic cancer)
4 (disease)
8691 (mycosis fungoides)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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